[HTML][HTML] The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
Abstract Background The Environment Ontology (ENVO; http://www. environmentontology.
org/), first described in 2013, is a resource and research target for the semantically …
org/), first described in 2013, is a resource and research target for the semantically …
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges
Text mining in the biomedical sciences is rapidly transitioning from small-scale evaluation to
large-scale application. In this article, we argue that text-mining technologies have become …
large-scale application. In this article, we argue that text-mining technologies have become …
[HTML][HTML] PREGO: a literature and data-mining resource to associate microorganisms, biological processes, and environment types
To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in
which environments (where) and which microorganisms carry them out (who). Here, we …
which environments (where) and which microorganisms carry them out (who). Here, we …
[HTML][HTML] The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
Background The systematic analysis of a large number of comparable plant trait data can
support investigations into phylogenetics and ecological adaptation, with broad applications …
support investigations into phylogenetics and ecological adaptation, with broad applications …
[HTML][HTML] TraitBank: Practical semantics for organism attribute data
Encyclopedia of Life (EOL) has developed TraitBank (http://eol. org/traitbank), a new
repository for organism attribute (trait) data. TraitBank aggregates, manages and serves …
repository for organism attribute (trait) data. TraitBank aggregates, manages and serves …
Pancreatic cancer symptom trajectories from Danish registry data and free text in electronic health records
JX Hjaltelin, SI Novitski, IF Jørgensen, T Siggaard… - Elife, 2023 - elifesciences.org
Pancreatic cancer is one of the deadliest cancer types with poor treatment options. Better
detection of early symptoms and relevant disease correlations could improve pancreatic …
detection of early symptoms and relevant disease correlations could improve pancreatic …
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation
E Pafilis, PL Buttigieg, B Ferrell, E Pereira… - Database, 2016 - academic.oup.com
The microbial and molecular ecology research communities have made substantial
progress on developing standards for annotating samples with environment metadata …
progress on developing standards for annotating samples with environment metadata …
A guide to dictionary-based text mining
PubMed contains more than 27 million documents, and this number is growing at an
estimated 4% per year. Even within specialized topics, it is no longer possible for a …
estimated 4% per year. Even within specialized topics, it is no longer possible for a …
Overview of the interactive task in BioCreative V
Fully automated text mining (TM) systems promote efficient literature searching, retrieval,
and review but are not sufficient to produce ready-to-consume curated documents. These …
and review but are not sufficient to produce ready-to-consume curated documents. These …
[HTML][HTML] Seqenv: linking sequences to environments through text mining
Understanding the distribution of taxa and associated traits across different environments is
one of the central questions in microbial ecology. High-throughput sequencing (HTS) …
one of the central questions in microbial ecology. High-throughput sequencing (HTS) …